quantile_normalization.py

# simple implementation of quantile normalization? 
import numpy as np 

def quantile_norm(data):
    """
    Source: https://en.wikipedia.org/wiki/Quantile_normalization 

    Note: this doesn't deal with ties very well. 

    Args:
        data (array): dense array of shape (genes, cells_or_samples)

    Returns:
        new array with same shape as data, but after quantile normalization
    """
    rows, cols = data.shape
    normed_data = np.zeros(data.shape)
    orders = data.argsort(0).argsort(0) 
    data_sorted = np.sort(data, 0)
    ranks = data_sorted.mean(1)
    for c in range(cols):
        normed_data[:,c] = ranks[orders[:,c]] 
    return normed_data 
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